Genetic characterization and phylogenetic analysis of the S genes of porcine epidemic diarrhea virus isolates from China from 2020 to 2023

IF 2.5 4区医学 Q3 VIROLOGY

Archives of Virology Pub Date : 2024-08-16 DOI:10.1007/s00705-024-06109-0

Yi Wang, Jiali Qian, Yupeng Li, Dandan Wang, Xu Song, Shuo Tian, Jinzhu Zhou, Wei Wang, Rongli Guo, Jizong Li, Xuehan Zhang, Xianwei Wang, Baochao Fan, Bin Li

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Abstract

Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that has been the main cause of diarrhea in piglets since 2010 in China. The aim of this study was to investigate sequence variation and recombination events in the spike (S) gene of PEDV isolates from China. Thirty complete S gene sequences were obtained from PEDV-positive samples collected in six provinces in China from 2020 to 2023. Phylogenetic analysis showed that 10% (3/30) belonged to subtype GII-a, 6.67% (2/30) were categorized as subtype GII-b, 66.67% (20/30) were categorized as subtype GII-c, and 16.66% (5/30) were clustered with the S-INDEL strains. Amino acid sequence alignments showed that, when compared to strains of other subtypes, the GII-c strains had two characteristic amino acid substitutions (N139D and I289M). Five S-INDEL subtype strains had a single amino acid deletion (139N) and four amino acid substitutions (N118G, T137S, A138S, and D141G). Recombination analysis allowed six putative recombination events to be identified, one involving recombination between GII-c strains, two involving GII-c and GII-b strains, two involving GII-c and GI-a strains, and one involving GII-a and GI-b strains. These results suggest that recombination between PEDV strains has been common and complex in recent years and is one of the main reasons for the continuous variation of PEDV strains.

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2020-2023 年中国猪流行性腹泻病毒分离株 S 基因的遗传特征和系统发育分析。

猪流行性腹泻病毒（PEDV）是一种肠道冠状病毒，自2010年以来一直是导致中国仔猪腹泻的主要原因。本研究旨在调查中国 PEDV 分离物穗（S）基因的序列变异和重组事件。本研究从 2020 年至 2023 年在中国 6 个省份采集的 PEDV 阳性样品中获得了 30 个完整的 S 基因序列。系统进化分析表明，10%（3/30）属于GII-a亚型，6.67%（2/30）属于GII-b亚型，66.67%（20/30）属于GII-c亚型，16.66%（5/30）与S-INDEL株聚类。氨基酸序列比对结果显示，与其他亚型的菌株相比，GII-c 菌株有两个特征性的氨基酸置换（N139D 和 I289M）。五个 S-INDEL 亚型菌株有一个氨基酸缺失（139N）和四个氨基酸置换（N118G、T137S、A138S 和 D141G）。重组分析确定了六个假定重组事件，其中一个涉及 GII-c 株系之间的重组，两个涉及 GII-c 和 GII-b 株系，两个涉及 GII-c 和 GI-a 株系，一个涉及 GII-a 和 GI-b 株系。这些结果表明，近年来 PEDV 株系间的重组既普遍又复杂，是 PEDV 株系持续变异的主要原因之一。

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来源期刊

Archives of Virology 医学-病毒学

CiteScore

5.10

自引率

7.40%

发文量

324

审稿时长

4.5 months

期刊介绍： Archives of Virology publishes original contributions from all branches of research on viruses, virus-like agents, and virus infections of humans, animals, plants, insects, and bacteria. Coverage spans a broad spectrum of topics, from descriptions of newly discovered viruses, to studies of virus structure, composition, and genetics, to studies of virus interactions with host cells, organisms and populations. Studies employ molecular biologic, molecular genetics, and current immunologic and epidemiologic approaches. Contents include studies on the molecular pathogenesis, pathophysiology, and genetics of virus infections in individual hosts, and studies on the molecular epidemiology of virus infections in populations. Also included are studies involving applied research such as diagnostic technology development, monoclonal antibody panel development, vaccine development, and antiviral drug development.Archives of Virology wishes to publish obituaries of recently deceased well-known virologists and leading figures in virology.